The crux of the issue is a Reuters report from earlier this month that said the US government ordered Yahoo to build surveillance tools to scan through customer emails for intelligence information. Wednesday's letter, written by Yahoo General Counsel Ronald Bell, asks Clapper to confirm whether it did indeed issue an order, declassify it, and provide more context around it.

"Yahoo was mentioned specifically in these reports, and we find ourselves unable to respond in detail," Bell wrote.

The letter says those press reports, coupled with a lack of transparency from the government, has caused speculation about Yahoo and its "approach" to privacy.

"That speculation results in part from a lack of transparency and because US laws significantly constrain -- and severely punish -- companies' ability to speak for themselves about national security related orders even in ways that do not compromise US government investigations," Bell wrote.

Clapper's press office did not immediately return a request for comment.

The letter comes during a particularly turbulent time for Yahoo. Aside from the email-scanning controversy, the company also disclosed last month that it suffered a massive data breach in 2014 that resulted in the personal information from half a billion Yahoo user accounts being stolen.